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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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PTM-Sheperd Crash for Variable Citrullination Search #1795

Closed petersclarke closed 6 days ago

petersclarke commented 1 week ago

log_2024-09-24_19-12-25.zip

Hello - I'm processing fractionated data for arginine citrullination. No matter the combination of files I try to search, I receive the following error. It could be related to variable/fixed modifications being attributed to the same site. Thanks for any help you can provide!

"Finding spectral data Indexing data from 129 Fatal error: In dataset "129" could not find mzData for run 20240920..."

fcyu commented 1 week ago

It seems to be a bug.

My guess is that the _calibrated prefix in the file name broke the logic of locating the files because the _calibrated is a key word to mark a calibrated mzML file. Maybe PTM-Shepherd didn't expect the _calibrated_calibrated prefix after generating the calibrated mzML file.

Best,

Fengchao

dpolasky commented 1 week ago

Based on the run settings, I think you should not run PTM-Shepherd at all because there are no mass offsets in the search (so it will not do anything), and disabling it will avoid the crash. Though I think Fengchao is right about the source of the crash being the "_calibrated" in the raw file name, and we will still fix that for the next version.

Also it looks like you set the fragment mass tolerance to 0.3 Da, but (at least some of) the MS2 scans are high resolution so high res settings were used for the search. However, deisotoping was disabled automatically because of the low res initial setting, so fixing that setting should improve the results.

Best, Dan

dpolasky commented 1 week ago

Fixed in d5edb47

petersclarke commented 6 days ago

Great, thanks for the quick help. Clearing up those issues solved it for me.